[English] 日本語
Yorodumi
- PDB-1ksq: NMR Study of the Third TB Domain from Latent Transforming Growth ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ksq
TitleNMR Study of the Third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
ComponentsLATENT TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN 1
KeywordsPROTEIN BINDING / latent transforming growth factor-beta binding protein-1 / LTBP-1 / TGF-beta / TB domain / latency associated propeptide / LAP
Function / homology
Function and homology information


: / sequestering of TGFbeta in extracellular matrix / protein metabolic process => GO:0019538 / microfibril / microfibril binding / transforming growth factor beta receptor activity / coronary vasculature development / transforming growth factor beta binding / aorta development / Molecules associated with elastic fibres ...: / sequestering of TGFbeta in extracellular matrix / protein metabolic process => GO:0019538 / microfibril / microfibril binding / transforming growth factor beta receptor activity / coronary vasculature development / transforming growth factor beta binding / aorta development / Molecules associated with elastic fibres / ventricular septum development / extracellular matrix / post-translational protein modification / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / collagen-containing extracellular matrix / endoplasmic reticulum lumen / calcium ion binding / protein-containing complex / extracellular region
Similarity search - Function
TB domain / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site ...TB domain / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Latent-transforming growth factor beta-binding protein 1 / Latent-transforming growth factor beta-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLack, J. / O'leary, J.M. / Knott, V. / Yuan, X. / Rifkin, D.B. / Handford, P.A. / Downing, A.K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution Structure of the Third TB Domain from LTBP1 Provides Insight into Assembly of the Large Latent Complex that Sequesters Latent TGF-beta.
Authors: Lack, J. / O'leary, J.M. / Knott, V. / Yuan, X. / Rifkin, D.B. / Handford, P.A. / Downing, A.K.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LATENT TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)8,0601
Polymers8,0601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein LATENT TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN 1 / Transforming growth factor beta-1 binding protein 1 / TGF-beta1-BP-1


Mass: 8060.024 Da / Num. of mol.: 1 / Fragment: Third TB Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTBP1 / Plasmid: pQE30 / Species (production host): Escherichia coli / Gene (production host): LTBP1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22064, UniProt: Q14766*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
131HMQC-J
NMR detailsText: 3D NOESY mixing time 150ms 2D NOESY mixing time 90ms

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.7 mM [U-15N] TB3-LTBP-1, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21.2 mM [U-15N] TB3-LTBP-1, 99.9% D2Osample_299.9% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMTB3-LTBP-1[U-15N]1
1.2 mMTB3-LTBP-1[U-15N]2
Sample conditionspH: 5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA6001
GE OMEGAGEOMEGA7502

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure calculation
NMRView3.1.2Johnson, One Moon Scientificdata analysis
Felix2.3Accelrys Software Inc.data analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
Details: The structures are based on a total of 1676 restraints, 1610 NOE-derived distance constraints, 36 distance restraints for 18 hydrogen bonds, and 30 dihedral angle phi restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more